README.Rmd

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# DEP2

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DEP2 is a comprehensive analysis toolkit developed from the previous package DEP for mass spectrometry based proteomics data. It offers differential expression/enrichment analysis pipelines for various types of data, such as protein-level quantity (e.g. proteingroup), peptide-level quantity data, and modification-specific proteomics (quantities of modified peptides). DEP2 not only encompasses functions for data processing, hypothesis testing (via limma), and visualization but also incorporates a pipeline for aggregating peptides into proteins. To reduce the barrier in omics analysis, downstream functional explorations are packaged as suites, including functional enrichment, timecourse cluster and protein-protein interaction network. DEP2 also contains an an easy-to-use shiny application designed with modularization.

## Installation

You can install DEP2 from [GitHub](https://github.com/mildpiggy/DEP2) using the following command:

```{r, eval=FALSE}
# install.packages("devtools")
devtools::install_github("mildpiggy/DEP2")
```

Please note that DEP2 requires an R version higher than 4.1.0. We recommend installing the latest R version from scratch to avoid any compatibility issues with dependent packages. Additionally, for Apple Mac, please make sure to have the [Fortran](https://mac.r-project.org/tools/) compiler installed as it is necessary for some dependencies. 

## Check the suggested packages required in analysis

By default, DEP2 is installed with the essential dependent packages. However, certain analysis modules may require additional suggested packages. Users can run the following commands to complete the functionality of DEP2:

```{r example,eval=FALSE}
library(DEP2)

# Check and install required packages for enrichment analysis.
DEP2::check_enrichment_depends(install = TRUE)

# Check and install the appropriate Anotation OrgDb for Human.
DEP2::check_organismDB_depends(organism = "Human",install = TRUE)
# The 'organism' parameter can also be specified with other species names, like Mouse, Rat. 

# Check and install required packages for PPI analysis.
DEP2::check_PPI_depends(install = TRUE)

# Check and install required packages for RNA-seq analysis.
DEP2::check_RNAseq_depends(install = TRUE)
```

Alternatively, you can install DEP2 with all suggested packages using the following command:

```{r example2,eval=FALSE}
devtools::install_github("mildpiggy/DEP2", dependencies = TRUE)
```

## Run shiny application

To run the built-in shiny application, use the run_app function:

```{r, eval=FALSE}
library(DEP2)
DEP2::run_app()
```


## Further information

For more information and details on the functionalities of DEP2, you can visit the online [website](https://mildpiggy.github.io/DEP2/) or refer to the built-in vignette after installation.

## Citation

If you use DEP2 in your publication, please cite the articles.

```{r, eval=T,comment = ">",collapse=F}
citation("DEP2")
```